The spatial organisation of soils is crucially important in affecting belowground function, and the associated delivery of ecosystem services. Fungi constitute an important part of the soil biomass. As well as playing key roles in nutrient cycling and biotic interactions, they are also intimately involved in soil structural dynamics. Fungi mediate the formation of soil structure at a variety of spatial scales via charge, adhesive and enmeshment mechanisms. They also produce large quantities of hydrophobic compounds that affect water infiltration properties of soils. Fungi can also destroy soil structure via decomposition of organic matter that affects soil aggregation. In turn, soil structure affects fungi. The filamentous growth-form of fungi is a very efficient spacefilling structure well adapted for life in a spatially heterogeneous environment such as soil, but the labyrinthine pore network ultimately regulates how fungal mycelia grow through and function within the soil. The distribution of water within soils plays a crucial role in governing fungal development and activity, as does the spatial distribution of nutrient resources. This article reviews the continual interplay that occurs between soil structure and fungi, and discusses how self-organisation mechanisms may operate in the soil system.

‘Geomycology’ can be defined as the impact of fungi on geological processes, including the alteration and weathering of rocks and minerals, the accumulation of metals and their role in nutrient cycling and influence on proliferation of microbial communities in mineral substrates. Although many studies on microbial interactions with minerals have been published in recent years, the main focus of geomicrobiology has been on prokaryotes. Recently, it has become apparent that epi- and endolithic fungi comprise a significant component of the microflora in a wide range of rocks including siliceous types (silica, silicates and aluminosilicates), sandstone, granite, limestone, marble and gypsum. However, to date little is known about their in situ growth patterns or biogeochemical roles in such an environment. The aim of this article is to highlight our recent work on the biogeochemical roles of fungi inhabiting limestone (CaCO3) and dolomite (CaMg(CO3)2) rocks and to emphasise the importance of fungi as agents of geological change.

Most nematode-trapping fungi are dependent on specific hyphal structures on or in which nematodes can be trapped mechanically or by adhesion. These structures are a prerequisite for the ability of the fungus to invade a host and are thus crucial for survival as well as virulence. The diversity of trapping structures is large and highly dependent on the environment of the fungus. Within one single species, Arthrobotrys oligospora, not only adhesive nets are formed but also so-called conidial traps, hyphal coils around hyphae of other fungi, and appressoria in the rhizosphere of agricultural crops. In this article these structures and the conditions for their development are described. Since the trapping structures influence the survival and the virulence of their producer, it is important that we know more about the molecular background of their development and function. The application of genomics to understand the function and the development of infection structures, therefore, has substantially increased the potential of A. oligospora to become a model system for fungal morphogenesis.

European beech (Fagus sylvatica L.) is an important forest tree species which was always considered being nonproblematic with regard to its susceptibility to pathogens and insects. However during the past decade, in Europe and the north-eastern USA an increasing number of trees and stands were showing symptoms typical for Phytophthora diseases: increased crown transparency, abnormally small and often yellowish foliage, a dieback of the crown, tongue-shaped necroses of the inner bark and the cambium with tarry or rusty spots on the surface of the bark either extending up to 7m from the stem base (collar rot) or occurring isolated higher up the stem (aerial bleeding cankers), fine root destructions and necrotic lesions on suberized roots. Large-scale investigations on both continents using specific isolation methods and ELISA kits for detection, and morphological and physiological parameters as well as ITS-DNA sequence analysis for identification demonstrated that several Phytophthora species were regularly involved as inciting agents of the decline. The most important species were Phytophthora citricola, P. cambivora and P. cactorum in Europe, and P. inflata in the USA. Their pathogenicity to beech was shown by stem inoculation and soil infestation tests performed by various groups. A small-scale nursery survey in Germany revealed that beech fields are regularly infested with various Phytophthora species. Options for disease management and control are discussed, and an emphasis is put on the prevention of disease spread via infested nursery stock.

This article outlines the important biogeochemical roles that fungi play in the degradation, utilization and transformation of organic and inorganic substrates. Fungal populations are intimately involved in element cycling at local and global scales and such processes have major implications for living organisms, notably plant productivity and human health. While most attention has focussed on carbon cycling, the involvement of fungi in most other elemental cycles is emphasised. Some fungal transformations have applications in environmental biotechnology, e.g. in metal leaching, recovery and detoxification, xenobiotic and organic pollutant degradation, as well as result in adverse effects when these mechanisms are involved in degradation of foodstuffs, natural products and building materials. This account highlights the interdisciplinary approach that is necessary to further understanding of the important roles that fungi play in the biogeochemical cycling of elements, the chemical and biological mechanisms that are involved, and their biotechnological significance.

It has been known for a long time that fungi may transport substances in their hyphae. Experiments using radioactive tracer isotopes have greatly expanded our knowledge about translocation and have revealed that many fungi may circulate resources throughout their mycelia. This article outlines a conceptual framework for when and where net-translocation of resources takes place. Effects of substrate qualities, mycelial growth and activity as well as interactions with living plant hosts and other microorganisms are discussed and exemplified with experimental data. It is concluded that translocation from more or less remote parts of the mycelium enables fungi to colonise substrates with a low initial resource availability and to actively increase the resource availability in the substrates, turning the colonising mycelium from a resource sink into a source. Thus, translocation not only occurs in response to environmental heterogeneity, but also allows fungi to create heterogeneity in their growth environment.

Lichens are characteristically found in environments subject to extremes of temperature, desiccation and low nutrient status. Despite this sexual structures are often formed in abundance. The underlying mechanisms of sex in lichen-forming fungi are discussed, together with possible ecological reasons for the persistence of sexuality. Special features of lichen sex are highlighted including sex at the limits of life on earth in Antarctica, re-lichenization following sex and dispersal, and the perennial nature of lichen fruiting bodies.

The effects of mycorrhizal fungi have traditionally been considered within the rather narrow perspective of their effects on the mineral nutrition of individual plants. Most biologists are familiar with the idea that these symbiotic fungi may improve plant uptake of dissolved mineral nutrients. What other effects do these symbionts have? Research during the past 20 years has increasingly viewed symbiotic mycorrhizal associations between plants and fungi within a wider, multifunctional perspective. New molecular methods have been applied to investigate mycorrhizal fungal communities (Bruns & Bidartondo, 2002) and greater attention has been paid to their possible effects at the level of the plant community. As we have acquired greater knowledge about fungal species diversity, so we have become more aware of the potential functional diversity of mycorrhizal fungi. The new multifunctional perspective includes mobilisation of N and P from organic polymers, possible release of nutrients from mineral particles or rock surfaces via weathering, effects on carbon cycling, interactions with myco-heterotrophic plants, mediation of plant responses to stress factors such as drought, soil acidification, toxic metals and plant pathogens, as well as a range of possible interactions with groups of other soil microorganisms.

The genus Biscogniauxia, a member of the family Xylariaceae, has a worldwide distribution with over 50 taxa recognised. Biscogniauxia mediterranea is well known as the causative agent of charcoal canker in cork oak and is a serious problem in Portugal. Other species also cause canker under specific conditions. There is good evidence that these species occur in healthy living trees as endophytes and then become invasive under water stress conditions. The ability of B. nummularia, B. nothofagi and B. uniapiculata to cause cankers in Fagus, Nothofagus and Eucalyptus respectively is reported here.

Two closely related chemoecological groups of fungi, the ammonia fungi and the postputrefaction fungi, have been associated with the decomposition by-products of cadavers. Sporocarps have been observed in disparate woodlands across the world and often mark sites of graves. These groups of fungi provide visible markers of the sites of cadaver decomposition and follow repeated patterns of successional change as apparent decomposition proceeds. We suggest these phenomena may become a useful tool for crime scene investigation, forensic archaeology and forensic taphonomy.

Ectomycorrhizas (ECM) are dual organs formed between the terminal feeder roots of many plant species and certain soil fungi. The species richness and taxonomic diversity of ECM symbionts is impressive: ca. 7-10,000 fungal and ca. 8,000 plant species may be capable of forming ECM. The latter are the dominant components of forest and woodland ecosystems over much of the earths surface. The obligate nature of the symbiosis for ECM fungi has been brought into question by reports that some species produce sporocarps under field conditions in the absence of a host plant. We suggest that there is no unequivocal evidence to support this. The spread of tree roots is often underestimated and small, overlooked hosts such as dwarf Salix spp or sedges may explain the appearance of ECM sporocarps in vegetation apparently devoid of ECM hosts. Compared to plant material, the sporocarps of ECM fungi contain high concentrations of N and P. We show that it would take between 3 and 14 million mycorrhizal tips, or 1800 km of hyphae, to supply the N in one sporocarp of Boletus edulis. The mantle formed by the fungus over the root tip is the likely site of storage for the N and P required for sporocarp production, and we discuss the chemical and structural mechanisms developed on mantles by ECM fungi to defend this resource against fungivory.

Invasive hyphal growth allows filamentous fungi to insinuate themselves in the solid materials that serve as their food sources. Hyphae overcome the mechanical resistance of plant and animal tissues, and other substances through the secretion of digestive enzymes and the exertion of force. This force is derived from the osmotically-generated turgor pressure within the hypha and is governed by wall loosening at the growing apex. This article offers a concise description of the biomechanics of this process.

The majority of the 22 primate species known to eat fungi spend less than 5% of their feeding time doing so. The Goeldi's monkey (Callimico goeldii), a small South American primate, devotes up to 63% of its feeding time to the consumption of Auricularia auricula, A. mesenterica, Ascopolyporus polyporoides and A. polychrous. This may be as much as 6.1kg/animal/year of fresh weight of fungus consumed by an animal weighing half a kilogram; in comparison, the average person in the U.S.A. consumes 1.9 kg/person/year of fresh weight of mushrooms. The nutritional benefits of mycophagy appear to be relatively few, but need to be investigated further. Mycophagy by Goeldi's monkeys may be a strategy for reducing feeding competition during the dry season and likely affects the monkeys' home range size and distribution pattern.

The striking reddish-pink colour of the phylloplane yeast Sporobolomyces roseus was found to be due to three major carotenoid pigments which were identified by UV and mass spectra as β-carotene, torulene and torularhodin. Simple protocols for the extraction of these pigments and their visual separation by thin-layer chromatography are presented. Ultrastructurally, the pigments were localized within numerous small lipid droplets. Putative physiological roles and the biotechnological relevance of carotenoids from red yeasts are discussed.

Fungi play a key role in ecosystem nutrient cycles by scavenging, concentrating, translocating and redistributing nitrogen. To quantify and predict fungal nitrogen redistribution, and assess the importance of the integrity of fungal networks in soil for ecosystem function, we need better understanding of the structures and processes involved. Until recently nitrogen translocation has been experimentally intractable owing to the lack of a suitable radioisotope tracer for nitrogen, and the impossibility of observing nitrogen translocation in real time under realistic conditions. We have developed an imaging method for recording the magnitude and direction of amino acid flow through the whole mycelial network as it captures, assimilates and channels its carbon and nitrogen resources, while growing in realistically heterogeneous soil microcosms. Computer analysis and modeling, based on these digitized video records, can reveal patterns in transport that suggest experimentally testable hypotheses. Experimental approaches that we are developing include genomics and stable isotope NMR to investigate where in the system nitrogen compounds are being acquired and stored, and where they are mobilized for transport or broken down. The results are elucidating the interplay between environment, metabolism, and the development and function of transport networks as mycelium forages in soil. The highly adapted and selected foraging networks of fungi may illuminate fundamental principles applicable to other supply networks.

The genus Fusarium is surely known by everyone who looks at moulds associated with plants and soil, especially with its characteristic hyaline, multiseptate, slightly curved macroconidia. Nevertheless, it still seems a daunting task identifying isolates to species. The complexity of the genus is reflected in the number of ascomycete genera such as Nectria, Calonectria and Gibberella, which have Fusarium as the anamorph state. On the other hand many species of Fusarium have no known teleomorph. Colin Booth, President of the BMS in 1977, produced an invaluable monograph on the genus (Booth, 1971) and later, reviews by Nelson et al. (1983) and Gerlach & Nirenberg (1982) also help to make the genus more accessible.

Confusion still surrounds the identify and even the common name of the causal agent of frosty pod rot of cocoa, nearly 70 years after its placement in the genus Monilia, and over 20 years since its transfer to the new genus Moniliophthora, which was erected to accommodate what was considered to be a basidiomycete anamorph. Based on molecular and cytological evidence, we confirm that the fungus belongs in the Basidiomycotina and is closely related to the witches' broom pathogen of cocoa, Crinipellis perniciosa (Tricholomataceae: Agaricales). However, the only known reproductive stage in the life-cycle does not, in fact, represent the anamorph since meiosis occurs during sporogenesis and germination. The meiospore is interpreted to be a radically modified basidium, which performs a sexual, dispersal and resting function. The genus Moniliophthora, therefore, can no longer be maintained and must be reduced to synonymy with Crinipellis. The new combination, Crinipellis roreri, is proposed.

The long tubular branching hypha is the most important fungal growth form, although some fungi grow as discrete spherical or ellipsoidal yeast cells. Vacuoles are ubiquitous in yeast cells as well as in hyphae of filamentous fungi and can be readily stained by simple methods of dye uptake. They appear as spherical or tubular organelles of extremely variable size. Vacuoles are known or suspected to play several crucial roles in the physiology of vegetative growth. Only some of these roles are related to the activity of lytic intravacuolar enzymes. Thus, vacuoles can degrade redundant organelles, presumably recycling macromolecules, especially under conditions of nutrient starvation. They are also the destination of endocytotic vesicles originating by inward budding of the plasma membrane, thereby providing a mechanism of ‘face-lifting’ of the plasma membrane and a means of communication with the extracellular environment. Further, vacuoles store organic and inorganic nutrients, and they may detoxify the cytoplasm by sequestration of toxic substances.

When a major wild bird food producer advised, in their catalogue for the year 2000, that they could not offer peanuts because of the high levels of aflatoxin, the phenomenon of mycotoxins had really come into the public domain. In 2001 the same company was able to advise that 'Although present in some peanut crops this season, aflatoxin is not currently creating any major peanut supply problems'. Mycotoxins, and specifically peanuts and the health of wild birds, were reviewed in earlier volumes of this journal (Isaac 1994 a, b) but the passage of time has not led to any reduction in the problems associated with the presence of mycotoxins in foods and animal feeds. Indeed, the improvement in analytical methods, and the implications of legislation in many countries have served to increase awareness of mycotoxins.

Fungi can be found in almost any environment, and play important roles in ecosystem processes such as nutrient cycling and degradation. Despite their importance, the vast majority of fungi have not yet been isolated and identified. Due to the difficulties inherent in culture-based methods, fungal ecologists have turned to community fingerprinting techniques, which utilise signal molecules to profile the fungal members of an environmental sample without culturing. Commonly used signal molecules include chitin, ergosterol, membrane lipids and nucleic acids. Several DNA-based fingerprinting methods have been successfully applied to fungal communities, including D/TGGE (denaturing/temperature gradient gel electrophoresis), SSCP (single-stranded conformational polymorphism), RISA (ribosomal intergenic spacer analysis), and T-RFLP (terminal restriction length fragment polymorphism). These techniques allow the fungal ecologist to rapidly profile fungal populations in an ecosystem, without the need for laborious culturing or cloning.